Download SBI-4U1 Exam Review

SBI-4U1 Exam Review
Biochemistry
1. Name and draw the functional groups discussed in class
Not sure of all the ones you did /did not discuss but check out this list here:
http://www.3rd1000.com/funcgrup/funcgrup.gif
2. Name and draw the linkages discussed in class
3. Draw structural formulas for the following: TO FOLLOW. TOO LATE FOR ME TO DRAW THESE
THINGS ON THE COMPUTER.
a. 1,4-dibromo-3-hexanol
b. propanoic acid
c. 2-butyl methyl ether (aka 2-methyoxybutane)
d. butyl propanoate
e. 3-ethyl-1-methyl-2-pentene
f. 6-bromo-4-propyl-2-hexyne
g. 3-chloro-butanamide
h. 1,3-dimethylcyclohexane
i. 1,3-dimethylbenzene
4. Name the following molecules:
a) butanoic acid
b) dimethyl ether
c) 1-bromo-2-methylcyclopentane
d) pentyl ethanoate
e) 1-bromo-5-methyl-2-hexene
f) 3-ethyl-2,4-hexadiyne
5. What is a structural isomer?
Same formula, different arrangement of atoms.
6. Give an example of a pair of structural isomers. Write their chemical formulas, and draw their
structural formulas.
Glucose and fructose, C6H12O6
7. Name and describe the biological macromolecules discussed in class. Include the following:
constituent monomers, linkages that join the monomers, and sketch an example of each.
Lipids (triglycerides) – fatty acid + glycerol, ester linkage
Nucleic acids – nucleotides, phosphodiester bond
Protein – amino acids, peptide linkage
Carbohydrates – monosaccharide, glycosidic linkage
Metabolic processes
1. What is the difference between passive transport, and active transport? Give an example of a
substance that is moved across the cell membrane by each of these methods.
Passive – moves substances along their concentration gradients; no energy required. Example: oxygen
into cells
Active – moves substances against their concentration gradients; energy is required. Example: sodium
potassium pump.
2. What is ATP, and how does it provide energy for cellular processes?
Adenosine triphosphate. Primary energy-providing molecule in a cell. Energy is released by hydrolyzing
the bond between the 2nd and 3rd phosphate groups.
3. What are oxidation and reduction? Give (general) examples of each.
Oxidation – Loss of electrons. Ex. Can also be loss of H, loss of energy, gain of O
Reduction – Gain of electrons Ex. Gain of H, gain of energy, loss of O
4. What type of macromolecule is an enzyme? What function does an enzyme have? How is it
important for metabolism?
Protein. Biological catalyst, specific to a certain substrate. Lowers the activation energy for reactions to
occur. Important because all metabolic reactions are catalyzed; would not occur without the presence
of an enzyme.
5. Name and describe the four stages of cellular respiration, in order.
What goes into each stage? What comes out of each stage? What coenzymes are involved?
Where does each stage occur? How is this stage important for the overall goal of cellular
respiration?
Glycolysis
In
glucose
Pyruvate ox.
pyruvate
Krebs
Acetyl coA
ETC
Electrons
(from FADH2,
NADH)
Out
pyruvate,
ATP,
NADH
Acetyl coA
CO2
NADH
CO2,
ATP
NADH
FADH2
ATP
NAD+
FAD
Coenzymes
NAD+
Where
Cytoplasm
NAD+
Mitochondrial
matrix
NAD+
FAD
Mitochondrial
matrix
Inner
membrane
Importance
Breaks C-C
bonds of
glucose and
stores the free
energy in
NADH and
FADH2
Minimal ATP
production
Bulk of ATP is
produced via
chemiosmosis
6. In what stage is most of the ATP synthesized in cellular respiration, and by what enzyme?
Electron transport/chemiosmosis. ATP synthase.
7. What force drives the bulk synthesis of ATP as described above?
Electrochemical gradient (proton-motive force)
8. What is the overall equation for cellular respiration?
C6H12O6 + O2  6CO2 + 6H2O + energy
a. Where is each of the reactants utilized?
Glucose – Glycolysis
Oxygen – Electron transport chain – final electron acceptor
b. Where is each of the products produced?
Carbon dioxide – Pyruvate oxidation (2) and Krebs (4)
9. List the components of the electron transport chain, in order
NADH dehydrogenase, ubiquinone, cytochrome b-c1 complex, cytochrome C, cytochrome
oxidase complex
.
10. What is anaerobic respiration, and why does it occur?
Anaerobic “respiration” refers to alternative metabolic pathways that occur when oxygen is not
available.
11. Describe the two types of anaerobic respiration.
a. Ethanol fermentation – yeast, bacteria. Pyruvate is decarboxylated, then reduced by
NADH. End product: ethanol, and NAD+ is regenerated so glycolysis can continue.
b. Lactic acid fermentation – humans. Pyruvate is reduced by NADH. Product: lactic acid,
and NAD+ is regenerated.
12. Label the structures of a chloroplast:
13. Name and describe the two stages of photosynthesis.
14. What goes into each stage? What comes out of each stage? What coenzymes are involved?
Where does each stage occur? How is this stage important for the overall goal of
photosynthesis?
In
Out
Coenzymes
Where
Importance
Light reactions
Lightindependent
reactions
(Calvin cycle)
Light energy
H2O
CO2
ATP
NADPH
NADPH
ATP
O2
NADP+
G3P
NADP+
Thylakoid
membrane
Stroma
Stores solar energy as
chemical energy.
Produces the NADPH
and ATP required for
carb. Production
G3P is used to build
glucose monomers
15. Where does each of the two stages occur? Same as above
16. What is the overall equation for photosynthesis?
6CO2 + H2O + light energy  6O2 + C6H12O6
a. Where is each of the reactants utilized?
Carbon dioxide – Calvin cycle. Carbon is fixed by rubisco.
Water – Electron transport chain (light rxns) – Water is split by Z protein to replenish
electron deficit in photosystem I. Also Calvin.
Light energy – Photoexcitation in the ETC – photosystems I and II
b. Where is each of the products produced?
Oxygen – Electron transport chain. Produced when water is split.
Glucose – G3P from Calvin is used to synthesize glucose.
17. What is the pigment at the reaction centre of a photosystem, and what role does it play?
Chlorophyll a – absorbs energy, electrons get excited and pass along the ETC
18. What is the function of the pigments in the antenna complex of a photosystem?
Absorb other wavelengths of light and transfer their energy to chlorophyll a.
19. What is rubisco, and what reactions does it catalyze?
Must abundant enzyme in the world; catalyzes the fixation of carbon dioxide to RuBP in the
Calvin cycle. It also catalyzes the fixation of oxygen to RuBP (photorespiration).
20. What is a C3 plant?
A “typical” plant – one that produces a 3-C intermediate first in the Calvin cycle. Particularly
susceptible to photorespiration.
21. Describe the relationship between carbon dioxide concentration and photosynthetic rate in a C3
plant.
As the concentration of CO2 rises, the photosynthetic rate increases. This will occur until the
enzymes of the Calvin cycle are saturated, at which point a plateau will then occur. Generally,
the higher the concentration of ambient CO2, the higher the plateau
22. Describe the relationship between light intensity and photosynthetic rate in a C3 plant. (Include
a definition of the light-saturation point).
At low light intensities, light intensity limits the photosynthetic rate. The amount of NADPH and
ATP produced depends on availability of light. As light intensity increases, the light-saturation
point is reached: this is the point where light is no longer the limiting factor – it will be either
CO2 or temperature. The Calvin Cycle enzymes are saturated so increasing NADPH and ATP will
not increase the overall rate of photosynthesis.
23. List the components of the photosynthetic electron transport chain, in order.
Photosystem I, plastoquinone (Q cycle), b6-f complex, plastocyanin, photosystem II, ferredoxin,
NADP reductase
24. Mitochondria and chloroplasts have a structural feature in common: what is this feature?
Double membrane structure (inner and outer). Ideal for building up H+ reservoir for chemiosmosis
25. What is the endosymbiotic theory? Describe how each partner in the symbiotic relationship
would benefit from this type of relationship.
The theory that mitochondria and chloroplasts were once free-living organisms that were
engulfed by a primitive cell. Supported by independent genomes and replication machinery.
Host cell benefits from the energy produced by mitochondria, and the glucose generated by
chloroplasts. Engulfed organelle has the benefit of shelter and safety.
Molecular genetics
1. What is the difference between mitosis and cytokinesis?
Mitosis = The division of the nucleus.
Cytokinesis = the division of the cytoplasm, organelles, and membrane.
2. Describe the structure of DNA.
Two strands of deoxyribonucleotides, hydrogen bonded together, and running anti-parallel to
one another. Nucleotides are connected by phosphodiester bonds between the sugars and
phosphates. Molecule twists into a helical shape.
3. What is complementary base-pairing?
Bases of opposite strands pair predictably. Each pair contains one purine and one pyrimidine.
A-T
G-C
In RNA, A pairs with Uracil instead of with T
4. What is the central dogma of molecular biology?
DNA  RNA  protein
5. Complete the following table by describing the events of each process:
DNA replication
Transcription
Translation
Initiation
Helicase unzips the
double strands.
Polymerase III binds
RNA Polymerase
recognizes a promoter
sequence and binds
Ribosome recognizes 5’
cap in eukaryotic mRNA
and binds
Elongation
DNA Pol III adds free
nucleotides in the 5’ to
3’ direction
RNA Pol adds free RNA
nucleotides in the 5’ to
3’ direction
Amino acids are
brought to the
ribosome by tRNAs
Termination
DNA Pol falls off
RNA Pol recognizes a
specific termination
sequence
Stop codon is
recognizes. Ribosome
disassembles.
6. Name the enzymes involved in DNA replication, and list their functions.




DNA helicase - Breaks H-bonds between DNA

strands
DNA gyrase – Relieves tension caused by DNA

strands unwinding around each other. Does this
by cutting and re-ligating the DNA strands.
single-stranded binding proteins – Binds to the
unpaired bases once helicase unwinds the
strands. Prevents re-annealing of strands
RNA primase - Produces small RNA primers to
provide a free 3’ end for elongation to occur


DNA polymerase III – Adds on
deoxyribonucleotides to form a new DNA strand.
DNA polymerase I – Removes RNA primers and
replaces them with deoxyribonucleotides. Also
proofreads the newly-formed strand. Excises any
erronenously-incorporated nucleotides and
replaces them with correct ones.
DNA ligase – Forms phosphodiester bonds to join
the sugar phosphate backbones of DNA strand
fragments.
DNA telomerase – In prokaryotes, and in
eukaryotic germ line cells, prevents the shortening
of telomeres during successive rounds of
replication.
7. Name the enzymes involved in transcription, and list their functions.
RNA polymerase – Unwinds the DNA. Adds ribonucleotides to the growing strand
8. How does the information in mRNA direct the production of a polypeptide? What
organelles/molecules are involved in this process? What is the name of this process?




mRNA is read in triplets called codons
codons dictate the amino acids that are to be incorporated
ribosome reads the codons, tRNA brings appropriate amino acid
process is translation
9. What is the genetic code? What does it mean to say that the genetic code is “redundant”?
The genetic code is the “translation” dictionary from RNA to amino acid.
10. How is protein synthesis different in a eukaryotic cell, as compared with a prokaryotic one?
Eukaryotes – Possess membrane-bound organelles. Transcription and translation occur in separate
parts of the cell. Post-transcriptional modifications are required, and the ribosome recognizes the 5’
cap on the transcript.
Prokaryotes – Transcription and translation are coupled. Prokaryotic genes lack introns and are not
processed after transcription. The ribosome recognizes a sequence called the Shine Dalgarno
sequence.
11. Name and describe the types of point mutations.
Insertion – A base is inserted
Deletion – A base is deleted
Substitution – A base is switched out for another
12. What is a frameshift mutation? Which type(s) of point mutations can result in a frameshift?
A mutation that results in a shift of the reading frame. Insertions and deletions can result in a
frameshift.
13. What are silent, nonsense, and missense mutations?
Silent – No effect on protein structure
Nonsense – One amino acid is substituted for another.
Missense – A codon is converted into a stop codon. Protein synthesis is prematurely truncated.
14. Gel electrophoresis is a method that separates DNA fragments according to their sizes,
measured in base pairs (or kb – 1000 bp), within a gel matrix:
a. What causes the migration of fragments?
A current is applied.
b. In which direction will fragments migrate?
DNA is negatively charged. It will migrate away from the negative electrode, towards the
positive.
c. Which fragments will migrate the farthest?
The smallest will migrate farthest.
15.
a. What is recombinant DNA?
A fragment of DNA composed of DNA from two or more different sources.
b. Describe the following, and how they are used in producing recombinant DNA:
i. Restriction endonucleases
“Molecular scissors” – Cut desired DNA fragments
ii. DNA ligase
“Molecular glue” – Ligate fragments together by forming phosphodiester bonds
between the backbone fragments
iii. Plasmids
Serve as vectors – vehicles for carrying the recombinant DNA into a biological
system where it can then be transcribed and translated.
c. Describe two applications of recombinant DNA.
Producing synthetic proteins, such as insulin.
Conferring pesticide resistance to plants.
16. What is Hardy-Weinberg equilibrium, and what is the equation that describes it? Make sure to
define all of the variables and terms in the equation.
States that allele frequencies do not change from generation to generation, within a population.
p2 + 2pq + q2 = 1
p2 = genotype frequency of homozygous dominant (AA)
2pq = genotype frequency of heterozygous Aa
q2 = genotype frequency of homozygous recessive (aa),
where p = allele frequency of A and q = allele frequency of a
17. Two alleles for a locus A exist in a population: A and a. Homozygous dominant individuals make
up 49% of the population.
a. What are the allele frequencies for A and a?
AA = p2 = 0.49  p = 0.7
Therefore allele frequency of A is 0.7, or 70%
Allele frequency of a is 1-0.7 = 0.3 = 30%
b. How much of the population is Aa, and how much is aa?
Aa = 2pq = 2(0.7)(0.3) = 0.42 or 42%
aa = q2 = (0.3)2 = 0.09 or 9%
18. What conditions must be met in order to maintain Hardy-Weinberg equilibrium?
 large population
 equal mating opportunities
 no mutations occur
 no migration occurs
 no natural selection
19. Recombination of alleles is the "mixing up" of parental alleles during gamete formation, to
produce entirely new combinations of alleles.
a. What are "linked" genes?
Genes that tend to be inherited together i.e. not independently of one another.
b. By what two different processes can recombination occur?
Crossing over, aka homologous recombination (meiosis I) and Independent assortment
c. How does recombination occur for genes that are linked?
Crossing over
d. How does recombination occur for genes that are unlinked?
Independent assortment
20. Draw the linkage map, with map distances, for the following four loci: A,B,C,D:
A-B
A-D
A-C
54%
30%
18%
B-C
C-D
57%
12%
Locus B has a recombination frequency of 54% with A, and 57% with C, meaning it is not linked to
either gene. It is on a separate chromosome. A, C, and D are all on the same chromosome:
Chromosome 1: A
18 mu
C
12 mu D
Chromosome 2: B
Homeostasis
1. Draw a rough sketch of a nephron, with labelled parts.
b: bowman’s capsule
c: proximal tubule
i: descending loop of Henle
g: ascending loop of Henle
d: distal tubule
e: collecting duct
2. The nephron is designed to produce concentrated urine. How does it accomplish this? What
role is played by the arrangement of the nephron tubules, and the permeabilities of the various
parts?
The ascending loop of henle is permeable to Na, but not to water. The descending limb is permeable to
water, but not to Na.
Na is actively transported out of the nephron in the ascending LoH. This raises the osmotic pressure
(solute concentration) of the surrounding interstitial fluid. Water leaves the descending limb by
osmosis.
Filtrate that travels down the descending limb, deep into the medulla of the kidney, is increasingly
concentrated so that lots of Na is pumped out near the bottom. A concentration gradient is established
in the interstitial fluid. As filtrate then travels down the collecting duct towards the ureter, ALOT of it
leaves due to the osmotic pressure outside the nephron.
In a nutshell: Active transport of Na establishes an osmotic pressure that draws water out of the
nephron. The osmotic pressure is greatest in the medulla, and gradually decreases up into the cortex.
As the collecting duct “PLUNGES” down into the medulla once again, water diffuses out by osmosis to
produce concentrated urine.
3.
a. What substances are filtered from the glomerulus into the Bowman's capsule? What
substances are not?
Filtered: Water, NaCl, glucose, amino acids, urea, H+, minerals
Not filtered: plasma proteins, white blood cells, platelets
b. What substances are reabsorbed by the nephron?
Na, Cl, HCO3, glucose, amino acids (most of it in the proximal tubule)
c. For substances that are not reabsorbed, why do their concentrations increase after
filtration?
Concentration of a substance is the amount of solute per volume. When water leaves
the tubule by osmosis, the volume decreases. Since the amount of solute is the same,
the concentration increases since there is less solvent.
4. What two enzymes does the pancreas produce, and what are their effects?
Insulin – Makes cells permeable to glucose. Blood glucose levels decrease
Glucagon – Converts conversion of glycogen to glucose. Blood glucose levels increase
5. Draw a tough sketch of a nerve cell, with labelled parts.
6. What ion initiates an action potential in a nerve?
Sodium.
Gated sodium channels are opened as a result of either a disturbance in membrane potential
(voltage-gated Na channels) or binding of a neurotransmitter (ligand-gated Na channels).
7. What prevents an action potential from being sustained?
Where acetylcholine (ACh) is the neurotransmitter that transmits messages across the synapse,
cholinesterase, released by the post-synaptic neuron, will destroy ACh so that the cell can be
repolarized.
Forebrain
Cerebrum
8. Copy and complete the following table about the parts of the brain
Region Structure
Controls
Frontal lobe
Inhibition of unsuitable behaviours; Personality
Temporal lobe
Vision, hearing, memory
Parietal lobe
Vision
Hypothalamus
Midbrain
Hindbrain
Occipital lobe
Touch, Emotions
Midbrain
Signals the pituitary; Often the bridge between
the nervous and endocrine systems.
Relays vision and hearing information to the
cerebrum
Cerebellum
Limb movements, Balance
Pons
Passes info through hindbrain
Medulla oblongata
Controls involuntary muscle action
9. Label the indicated structures of the brain:
Population dynamics
1. What is population density? What equation is used to calculate population density? Make sure
to define all variables.
Number of individuals of a species per given area.
D = N/S, where D = population density; N = number of individuals; S = space occupied by
population
2. Ecologists use mark-recapture analysis to estimate the number of individuals in a population.
What equation is used to estimate population size? Make sure to define all variables.
N = (Mn)/m, where N = total population; M = Total number marked; n = Size of second sample;
m = number of recaptures
3. To estimate the deer population in a 2.0 ha by 8.0 ha area in a forest in southern Ontario, 175
deer were captured and tagged with bands.
a. After three weeks, 135 deer were recaptured, and 21 had bands. Estimate the
population of deer in this forest.
M = 175; n = 135, m = 21
N = (175 x 135) / 21 = 1125
b. Calculate the population density.
N = 1125; S = 16.0 ha2
D = N/S = 1125/16.0 = 18.75 deer/ha
4. What is the difference between a density-dependent factor, and a density-independent factor?
Give an example of each.
Both influence population regulation, but the influence of a density-dependent factor will intensify
as population density increases. The effect of a density-independent factor does not depend on
population density.
Dependent: Disease, Food availability
Independent: Natural disaster (e.g., flood)
5. Briefly describe the following types of interactions:
a. Competition – Individuals try to obtain the same resources. Can be interspecific
(individuals of different species) or intraspecific (same species)
b. Predation – Individual of one species hunts and kills another for food.
c. Parasitism – An interaction that is beneficial to one species, and harmful to another (the
host). The host usually does not die.
d. Mutualism – Both individuals benefit.
e. Commensalism – One individual benefits, the other is not affected in any way.
6. Which trophic level (link in the food chain) contains the highest amount of energy?
Producers (First trophic level - plants)
7. What is bioaccumulation?
The tendency for pesticides and other toxins to accumulate at higher concentrations in
organisms high up on the food chain. Occurs because a predator will eat many prey, in the
process absorbing all the toxins their bodies contained.
8. What is desalinization? What prevents it from being a method of increasing the water supply?
Desalinization is the removal of salt from salt water.
Distillation – Boiling water, and then collecting condensed vapour
Reverse osmosis – Uses high pressure to pump water through a membrane
Cons: Very expensive. Large amounts of salt produced, and nowhere to put the salt.
9. Choose one of the following ecological problems and discuss it briefly: SEE BOOK/ISU
a. Food sources (farming/fisheries)
b. Greenhouse effect and global warming
c. Water supply
d. Desertification and deforestation
Essay questions
You are allowed to bring a rough draft into the exam. If you do so, it must be submitted with the exam.
Your answer must be in essay format with complete sentences and paragraphs. Content, organization,
grammar and spelling all count.
1. Discuss the reasons why the development of: proteins and nucleic acids, O2 utilization, and the
electron transport chain were important steps in the evolution of organisms.
2. Explain the role of restriction endonucleases, DNA ligase, plasmids, sticky and blunt ends in producing
recombinant DNA. Also explain the benefits of recombinant DNA.
3. Cellular respiration and photosynthesis are closely related processes made possible by the unique
structures in which they occur. Discuss this statement. (The proton pump and endosymbiosis could be
discussed in this essay.)
4. SITUATION: It is March Break and a group of Redmond students have arrived in Florida. It was an
evening flight so they arrive at the hotel by 7:00am. Tara has a quick breakfast and then grabs a lounge
chair by the pool. She remains there for most of the day when she is not swimming by the pool. Discuss
the mechanisms used by the nervous, endocrine and excretory systems to deal with this situation and
discuss other systems involved like the muscular, digestive and circulatory systems. Make sure you
discuss feedback mechanisms.
5. There are different types of ecological competition. Discuss the following types and explain examples
in each case: interspecific competition, intraspecific competition, interference competition, exploitative
competition, resource partitioning.